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- PDB-4x1w: Crystal structure of unbound RHDVb P domain -

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Basic information

Entry
Database: PDB / ID: 4x1w
TitleCrystal structure of unbound RHDVb P domain
ComponentsVP1
KeywordsVIRAL PROTEIN / Major Capsid Protein / Capsid spike / Protruding domain / Dimer / HBGA binding
Function / homologyCalicivirus coat protein / Calicivirus coat protein / VP1
Function and homology information
Biological speciesRabbit hemorrhagic disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLeuthold, M.M. / Hansman, G.S.
CitationJournal: J.Virol. / Year: 2015
Title: Structural analysis of a rabbit hemorrhagic disease virus binding to histo-blood group antigens.
Authors: Leuthold, M.M. / Dalton, K.P. / Hansman, G.S.
History
DepositionNov 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP1
C: VP1
D: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,39813
Polymers136,9194
Non-polymers4799
Water16,232901
1
A: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6195
Polymers68,4602
Non-polymers1603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-25 kcal/mol
Surface area22780 Å2
MethodPISA
2
C: VP1
D: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7798
Polymers68,4602
Non-polymers3196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-27 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.190, 83.130, 118.290
Angle α, β, γ (deg.)90.000, 93.210, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 238 - 569 / Label seq-ID: 1 - 332

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D

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Components

#1: Protein
VP1


Mass: 34229.785 Da / Num. of mol.: 4 / Fragment: UNP residues 238-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabbit hemorrhagic disease virus / Gene: VP1 / Production host: Escherichia coli (E. coli) / References: UniProt: I7FLU3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 901 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: Lithium chloride, PEG 6000, Citric Acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984463 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984463 Å / Relative weight: 1
ReflectionResolution: 1.95→19.8 Å / Num. obs: 83210 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 20.24 Å2 / Rmerge F obs: 0.991 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.187 / Χ2: 0.945 / Net I/σ(I): 7.82 / Num. measured all: 384589
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-20.650.7681.3517449617860820.93598.4
2-2.060.7340.671.719077596859070.80199
2.06-2.120.820.6222.6928983587758670.69799.8
2.12-2.180.8570.5333.1728296565656530.59699.9
2.18-2.250.8850.4813.5626478547654680.5499.9
2.25-2.330.9110.4114.0724935532053080.46399.8
2.33-2.420.9290.3434.6423025513251110.38899.6
2.42-2.520.9480.325.5525162493649330.35799.9
2.52-2.630.9570.2856.2623807473847360.319100
2.63-2.760.9670.2337.5822184452545230.261100
2.76-2.910.9770.2038.5521335430543030.227100
2.91-3.080.9770.15710.2518711411541050.17899.8
3.08-3.30.9850.13812.4819612386238560.15499.8
3.3-3.560.9910.11414.6918037352535230.12799.9
3.56-3.90.9930.09616.8616614332733220.10799.8
3.9-4.360.9930.07718.8114084299729880.08799.7
4.36-5.030.9940.06919.712397262826200.07899.7
5.03-6.170.9960.0719.5111583225022490.078100
6.17-8.720.9960.06219.548356175717540.0799.8
8.720.9960.05223.9644649989020.05990.4

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4egt
Resolution: 1.95→19.798 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 4160 5 %
Rwork0.1798 79014 -
obs0.1814 83174 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.55 Å2 / Biso mean: 25.8415 Å2 / Biso min: 5.71 Å2
Refinement stepCycle: final / Resolution: 1.95→19.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9659 0 27 901 10587
Biso mean--29.71 30.48 -
Num. residues----1327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059960
X-RAY DIFFRACTIONf_angle_d0.98113677
X-RAY DIFFRACTIONf_chiral_restr0.0391536
X-RAY DIFFRACTIONf_plane_restr0.0051814
X-RAY DIFFRACTIONf_dihedral_angle_d11.0443386
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5900X-RAY DIFFRACTION7.499TORSIONAL
12B5900X-RAY DIFFRACTION7.499TORSIONAL
13C5900X-RAY DIFFRACTION7.499TORSIONAL
14D5900X-RAY DIFFRACTION7.499TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9499-1.97210.37451380.31052624276298
1.9721-1.99530.321340.29022534266898
1.9953-2.01960.32341380.28182625276399
2.0196-2.04510.29211380.26712617275599
2.0451-2.0720.30681360.259225932729100
2.072-2.10030.2861380.235626262764100
2.1003-2.13030.24931390.219126492788100
2.1303-2.16210.27141370.208926012738100
2.1621-2.19580.24991410.204326712812100
2.1958-2.23180.26161370.21426062743100
2.2318-2.27020.27991380.229726212759100
2.2702-2.31140.25321370.20926102747100
2.3114-2.35580.22561390.201826352774100
2.3558-2.40380.26121380.20462629276799
2.4038-2.4560.26291390.197626312770100
2.456-2.5130.24481380.196326312769100
2.513-2.57570.25031390.19326362775100
2.5757-2.64520.21431390.191726292768100
2.6452-2.72290.25321380.18726352773100
2.7229-2.81050.20091400.189226462786100
2.8105-2.91070.21261370.181226192756100
2.9107-3.02680.20511390.172326372776100
3.0268-3.1640.181390.162826442783100
3.164-3.33010.21541400.160626512791100
3.3301-3.53760.17121400.155226592799100
3.5376-3.8090.19241400.147126522792100
3.809-4.1890.1461400.132926572797100
4.189-4.78770.13641390.125726462785100
4.7877-6.0040.15141410.139626852826100
6.004-19.79850.16391440.152827152859100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.61554.22082.83656.83964.57913.0791-0.64270.42270.0446-0.79360.04970.03740.49430.01530.61170.38660.02030.01970.3147-0.01790.341623.6857-129.7578174.272
20.17650.23270.08811.98280.13610.8535-0.0475-0.0404-0.0414-0.0250.07660.0301-0.02720.0242-0.04110.1580.01740.00730.1959-0.01990.334127.6437-122.3926186.6333
33.8227-1.8916-2.49968.24056.05188.9751-0.1074-0.31620.1206-0.6337-0.02810.2223-0.75260.27510.1290.1750.0125-0.07570.2049-0.01350.382633.5878-103.881186.797
40.4533-0.5089-0.6974.08910.26563.4406-0.0314-0.41620.46550.26650.0064-0.26430.00390.05850.07750.1859-0.01060.01080.2013-0.04270.376337.4272-98.5938201.7994
54.9863-0.0742-0.21932.30072.45852.6266-0.25420.23390.9545-0.6748-0.34490.4058-1.07420.21650.52820.32110.0193-0.08560.24190.0220.346723.7515-103.2743185.23
61.25020.10070.00911.2977-0.20561.0916-0.0082-0.14470.06690.0648-0.04430.0748-0.072-0.08430.03690.16880.0225-0.00430.1816-0.04210.249436.0933-105.1858199.1837
71.15710.67630.15542.11070.19450.55630.0023-0.12160.01540.1081-0.02860.1434-0.0155-0.07150.03390.15050.02590.01790.1689-0.02020.210332.9187-118.546196.5051
83.9978-0.72094.42361.7224-1.25176.9998-0.02470.1657-0.34420.14620.0858-0.1698-0.02090.3058-0.06120.15690.00060.03210.1499-0.03140.320634.5437-125.0694188.6511
91.294-0.04480.75550.67190.47381.9058-0.0476-0.0708-0.1555-0.01790.00470.15730.0373-0.25030.03570.1755-0.01440.00930.2127-0.00680.404220.898-133.3111184.3648
102.74451.0454-0.55582.49490.65763.71350.0129-0.0266-0.22690.2049-0.05590.20920.2384-0.09330.01750.18420.00040.00980.13220.00260.318624.202-139.8721183.9318
116.659-0.87232.02711.3662.34726.19670.1748-0.05150.25670.1725-0.33190.34410.4564-0.80810.16540.1933-0.04850.02910.25720.04620.267437.1362-117.034168.3076
120.7998-0.1411.52582.9599-1.24373.12070.0774-0.0153-0.08060.0887-0.1366-0.0754-0.020.00580.06910.1191-0.01160.00920.1773-0.0130.242348.2191-117.9502168.751
135.97270.02192.7030.7354-0.82182.14110.0642-0.23-0.24250.0627-0.0785-0.2203-0.0805-0.02420.00820.14320.01390.03780.17190.01880.198559.3032-111.4058192.247
146.51213.99911.244.9311.81086.53660.3683-0.6016-1.34680.3479-0.49450.33071.07130.00940.09480.33010.0281-0.02240.22150.08080.50357.9653-126.8285182.7396
150.87370.0035-0.02840.8867-0.07461.6216-0.0524-0.0615-0.0157-0.00810.0278-0.0441-0.02520.02250.02450.14810.0103-0.02440.1644-0.00520.287658.561-109.7488187.176
160.76830.26830.83530.03120.29173.3305-0.0249-0.03610.1255-0.06440.03080.0205-0.2111-0.0081-0.00730.1619-0.00030.01190.15440.01190.263650.8595-108.3764173.0142
173.0411.16120.47877.409-0.33253.33550.29071.3169-1.0728-2.06440.28451.81850.9461-1.9892-0.71410.5979-0.0505-0.17790.7251-0.07670.563837.6529-97.3059179.2237
184.95681.0494-0.21692.8929-1.93748.1206-0.1199-0.18470.689-0.11260.1140.5882-0.5107-0.30370.01710.0730.0273-0.05280.2520.02290.318242.5178-107.9222171.2425
191.1480.59140.23972.751-0.94042.25520.03470.0401-0.0367-0.1329-0.03820.26350.0574-0.20140.00520.15480.0147-0.00660.2166-0.03480.255239.8123-117.3334158.886
204.9542-0.237-0.00388.8015-0.69574.9080.02110.30730.1224-0.0092-0.106-0.19160.1739-0.2970.06410.1533-0.0121-0.03330.2443-0.02470.189738.468-116.5369150.7228
219.53921.86725.80282.39120.31673.865-0.46440.45420.5159-0.5112-0.25090.3526-0.05560.1290.77020.36410.084-0.05360.229-0.02910.3726-1.409-138.8065113.7978
220.2018-0.2730.50922.6009-0.4851.1349-0.0526-0.0084-0.01450.01230.00560.0962-0.0617-0.11180.03510.1262-0.00830.02750.2073-0.0580.32460.7095-131.1782126.3619
234.0777-4.7466-4.12917.58496.91557.53350.3249-0.1035-0.0631-1.1234-0.40010.228-0.7715-0.06830.13140.2003-0.0023-0.00450.242-0.05350.35316.5103-112.2448127.3278
241.82410.58590.81011.8074-0.03732.0469-0.0582-0.11050.31810.0918-0.02490.3461-0.17160.02880.09880.13750.00820.03650.1977-0.0640.35775.7073-111.4428137.7169
252.44563.6218-1.5298.0475-2.45121.32860.0868-0.21910.04730.0978-0.18320.1197-0.1452-0.01510.08630.12750.0034-0.01710.1872-0.06030.259214.0164-111.7775137.1859
261.47980.69640.34951.19870.3860.64080.0111-0.21550.14470.1182-0.08590.14710.0274-0.14610.08350.1532-0.00780.02330.1929-0.03650.26774.8961-119.5345139.3516
275.4032.2622.27261.3990.70741.8852-0.105-0.1723-0.37880.06520.0120.15380.0191-0.10110.13850.1537-0.01210.01240.1358-0.03910.27038.3396-135.4658134.6099
280.04180.3030.14672.3987-0.31032.41130.0835-0.033-0.1699-0.13170.05740.23320.1433-0.3204-0.08690.1335-0.01120.02510.1853-0.03290.31772.3244-133.7512124.3988
290.4393-0.2374-0.41452.44950.68432.0802-0.02530.0156-0.2273-0.0114-0.05490.46060.155-0.1830.03960.1614-0.04560.01440.1913-0.01870.3877-3.2536-144.3282125.6619
305.29061.6835-3.05263.649-0.70267.5931-0.07770.01280.06790.06060.11460.32560.3701-0.3413-0.02120.187-0.01980.01980.1187-0.02730.2505-3.783-148.9871122.1906
316.7662-3.70831.68357.482-1.85136.3330.4308-0.01950.6485-0.1019-0.6084-0.060.705-0.19420.16030.24150.003-0.03240.27010.01040.35398.6596-132.2681102.8859
320.28510.21330.42491.71520.05122.5555-0.01770.04450.0585-0.0487-0.08080.0256-0.0964-0.13740.09960.12180.00830.00770.1854-0.00690.264719.8454-125.4693110.1752
335.9433-2.40316.86643.1788-2.80247.89770.45-0.4686-0.281-0.1078-0.185-0.46460.7414-0.4159-0.34290.2023-0.03490.01030.22210.00980.263125.3403-129.4817128.3203
342.16440.73520.57564.12912.77795.54190.002-0.14570.06860.1155-0.0565-0.195-0.22580.30740.01230.1232-0.0246-0.0210.14330.01880.260335.6586-116.5713136.209
354.72635.80412.40927.11112.8268.1886-0.118-0.3859-0.8713-0.05330.0373-0.54190.8051-0.6311-0.04860.2164-0.0069-0.00550.19860.06750.391430.9322-136.0802124.0953
360.8735-0.35890.29950.9693-0.01691.3471-0.01950.0039-0.07420.0322-0.0269-0.09910.00180.03190.05760.1214-0.0158-0.00940.13280.01890.251531.3563-119.0155129.1321
371.54110.3185-0.42670.88961.58763.53190.0143-0.00260.1594-0.2397-0.0387-0.0087-0.2363-0.07570.00510.18680.0183-0.0120.14580.0330.239723.3244-115.7013112.4793
381.88310.24941.04441.66290.41462.2661-0.07260.12370.0917-0.2154-0.09280.1763-0.261-0.21450.10880.16630.0576-0.01820.1875-0.03510.237715.4801-125.3907102.7116
394.4562.9575-3.64077.7057-2.27095.0480.15350.45220.7126-0.135-0.25380.7679-0.835-0.33970.10140.36360.0722-0.10670.29160.00250.297213.9727-112.5481100.291
404.44921.5034-2.06312.6720.57074.083-0.1830.2620.3733-0.1790.1050.2807-0.2405-0.31780.06640.24670.0672-0.07880.3022-0.02860.212211.5504-124.627292.8096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 237:243)A237 - 243
2X-RAY DIFFRACTION2(chain A and resid 244:290)A244 - 290
3X-RAY DIFFRACTION3(chain A and resid 291:299)A291 - 299
4X-RAY DIFFRACTION4(chain A and resid 300:324)A300 - 324
5X-RAY DIFFRACTION5(chain A and resid 325:331)A325 - 331
6X-RAY DIFFRACTION6(chain A and resid 332:410)A332 - 410
7X-RAY DIFFRACTION7(chain A and resid 411:475)A411 - 475
8X-RAY DIFFRACTION8(chain A and resid 476:500)A476 - 500
9X-RAY DIFFRACTION9(chain A and resid 501:545)A501 - 545
10X-RAY DIFFRACTION10(chain A and resid 546:569)A546 - 569
11X-RAY DIFFRACTION11(chain B and resid 237:257)B237 - 257
12X-RAY DIFFRACTION12(chain B and resid 258:290)B258 - 290
13X-RAY DIFFRACTION13(chain B and resid 291:319)B291 - 319
14X-RAY DIFFRACTION14(chain B and resid 320:330)B320 - 330
15X-RAY DIFFRACTION15(chain B and resid 331:413)B331 - 413
16X-RAY DIFFRACTION16(chain B and resid 414:472)B414 - 472
17X-RAY DIFFRACTION17(chain B and resid 473:479)B473 - 479
18X-RAY DIFFRACTION18(chain B and resid 480:494)B480 - 494
19X-RAY DIFFRACTION19(chain B and resid 495:553)B495 - 553
20X-RAY DIFFRACTION20(chain B and resid 554:569)B554 - 569
21X-RAY DIFFRACTION21(chain C and resid 238:244)C238 - 244
22X-RAY DIFFRACTION22(chain C and resid 245:290)C245 - 290
23X-RAY DIFFRACTION23(chain C and resid 291:300)C291 - 300
24X-RAY DIFFRACTION24(chain C and resid 301:344)C301 - 344
25X-RAY DIFFRACTION25(chain C and resid 345:372)C345 - 372
26X-RAY DIFFRACTION26(chain C and resid 373:456)C373 - 456
27X-RAY DIFFRACTION27(chain C and resid 457:475)C457 - 475
28X-RAY DIFFRACTION28(chain C and resid 476:508)C476 - 508
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30X-RAY DIFFRACTION30(chain C and resid 549:569)C549 - 569
31X-RAY DIFFRACTION31(chain D and resid 238:245)D238 - 245
32X-RAY DIFFRACTION32(chain D and resid 246:290)D246 - 290
33X-RAY DIFFRACTION33(chain D and resid 291:299)D291 - 299
34X-RAY DIFFRACTION34(chain D and resid 300:320)D300 - 320
35X-RAY DIFFRACTION35(chain D and resid 321:330)D321 - 330
36X-RAY DIFFRACTION36(chain D and resid 331:419)D331 - 419
37X-RAY DIFFRACTION37(chain D and resid 420:475)D420 - 475
38X-RAY DIFFRACTION38(chain D and resid 476:538)D476 - 538
39X-RAY DIFFRACTION39(chain D and resid 539:549)D539 - 549
40X-RAY DIFFRACTION40(chain D and resid 550:569)D550 - 569

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